Hi all,
So: I will try to keep it short but that's a bit tricky! Basically, my
problem is solved. But in the course of the week's computer related
trials and tribulations, I found out the following, which you may like
to know:
@Marco, well, we have a server to do intensive data work; my
colleague is using MZmine (2.0) on this system and it is set at 10GB JVM
memory. But I can't open .RAW files in that environment unfortunately
(UNIX). Also, if the JVM memory is not reaching its limit, why would it
help to move to a 64 bit system, the benefit of which I presume is so
the JVM memory can be increased? I later found out that we do in fact
have a similar windows based server, also 64 bit which was obviously a
well kept secret by our IT staff ;-) but as I will explain below, this
was not the problem.
@Tomas, well, I was originally using MZmine 1.97, because with
MZmine 2.0 I was unable to open .RAW files at all (I found this
initially strange given the two versions were installed on exactly the
same computer and so at the time abandoned using later versions). The
max no. of .RAW files I could open with 1.97 produced .scans files of
6.41gb total (208 .RAW files). I copied an extra 3.97gb of data into the
temp folder manually as a test as you suggested and this operation was
fine, so the temp folder itself didn't have a restriction there. I also
found, strangely, that if I converted the .RAW files to .cdf or mzXML
then I could open all 280 of my sample files (27gb .cdf files, or
6.7gb .mzXML files and 10.6gb scans files).
In the course of learning about the mzXML format and how to convert .RAW
files (I used msconvert on my computer as I read it is the latest
recommended version over ReAdw) - I had to make some updates to my
computer to get msconvert to run - installing .NET 3.5 sp1, a C + +
redistributable, MSFileReader.exe, loading various .dll libraries etc,
so I don't know which of these things made a difference, but now I find
that I can open .RAW files with MZmine 2.0 and 2.2. And with these
versions I can in fact open all 280 .RAW files. So - my problem solved!
I would like to test the system better with your 'creating lots of .RAW
files suggestion' but I'm afraid I don't know how to do it. I tried to
use the MZmine filter but then you can't export your cropped files as
individual .RAW files, just have them within the project, if I am
right! Even if I retrieved the cropped files from my .mzmine project
file then they are no longer in .RAW format so not a true test....as I
mentioned before MZmine 1.97 seemed to be able to handle lots of .mzXML
fine.
I also wanted to report that before I found out about our windows 64 bit
server and successfully managed to install mzMine 2.0 and 2.2 on my
local drive, you gave me the idea for the following workaround which I
managed to do successfully - I saved 3 smaller projects in MZmine 1.96,
containing between them all my .RAW files therefore in mzXML format and
spliced them together by going into the .mzmine file, unzipping it,
merging the mzXML and .scans files manually into one archive - and
rezipping them up again with a .mzmine extension. In this way I was able
to open them all at once in the MZMine (2.0) implementation on our UNIX
bioinformatics server, in a good format for me to inspect MSMS data as
well as the MS data (can't do it with .cdf files to my knowledge).
As you can see it is not easy for someone with limited computer
knowledge to get over all the irregularities that come up when using
very specialist software and implementing on lots of different systems!
But don't get me wrong, in our lab we are starting to really really like
MZmine and are trying to roll it out for all our students :-)
So, this story has a happy ending, but with all the -omics going on, I
imagine there will be lots of projects that need huge data handling
capacities - our next project has 750 samples, so will let you know if
we reach any limits with that!
Thanks for your time,
Chiarina
ps in the manual for 2.0 and 2.2 it says the thing needed for .RAW data
import is http://sjsupport.thermofinnigan.com/public/detail.asp?id=624
which is called 'Chromobj.dll'
but isn't it this link, to MSFileReader.exe??
http://sjsupport.thermofinnigan.com/public/detail.asp?id=703
I don't really know because I ended up installing both while I was
trying to get my various softwares to work, but I wanted to check with
you because I have to guide our IT guy in installing MZmine 2.2 on the
windows 64 bit server.
THANK YOU!!!
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